Simultaneous visualization of covalent and noncovalent interactions using regions of density overlap
P De Silva, C Corminboeuf - Journal of chemical theory and …, 2014 - ACS Publications
We introduce a density-dependent bonding descriptor that enables simultaneous
visualization of both covalent and noncovalent interactions. The proposed quantity is …
visualization of both covalent and noncovalent interactions. The proposed quantity is …
Revealing strong interactions with the reduced density gradient: a benchmark for covalent, ionic and charge-shift bonds
The visualization of covalent interactions has been a common practice in theoretical
chemistry thanks to the electron localization function (ELF). More recently, the reduced …
chemistry thanks to the electron localization function (ELF). More recently, the reduced …
Unraveling non-covalent interactions within flexible biomolecules: from electron density topology to gas phase spectroscopy
The NCI (Non-Covalent Interactions) method, a recently-developed theoretical strategy to
visualize weak non-covalent interactions from the topological analysis of the electron density …
visualize weak non-covalent interactions from the topological analysis of the electron density …
Computational characterization of the inhibition mechanism of xanthine oxidoreductase by topiroxostat
Xanthine oxidase (XO) is a member of the molybdopterin-containing enzyme family. It
interconverts xanthine to uric acid as the last step of purine catabolism in the human body …
interconverts xanthine to uric acid as the last step of purine catabolism in the human body …
LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields
EG Kratz, AR Walker, L Lagardère… - Journal of …, 2016 - Wiley Online Library
We introduce an initial implementation of the LICHEM software package. LICHEM can
interface with Gaussian, PSI4, NWChem, TINKER, and TINKER–HP to enable QM/MM …
interface with Gaussian, PSI4, NWChem, TINKER, and TINKER–HP to enable QM/MM …
Electronic structure theory to decipher the chemical bonding in actinide systems
JP Dognon - Coordination Chemistry Reviews, 2017 - Elsevier
The chemical bonding in actinide compounds is usually analysed by inspecting the shape
and the occupation of the orbitals or by calculating bond orders which are based on orbital …
and the occupation of the orbitals or by calculating bond orders which are based on orbital …
Leveraging QM/MM and Molecular Dynamics Simulations to Decipher the Reaction Mechanism of the Cas9 HNH Domain to Investigate Off-Target Effects
Y Maghsoud, VM Jayasinghe-Arachchige… - Journal of Chemical …, 2023 - ACS Publications
The clustered regularly interspaced short palindromic repeats (CRISPR) technology is an
RNA-guided targeted genome-editing tool using Cas family proteins. Two magnesium …
RNA-guided targeted genome-editing tool using Cas family proteins. Two magnesium …
The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems
It is well-known that the activity and function of proteins is strictly correlated with their
secondary, tertiary, and quaternary structures. Their biological role is regulated by their …
secondary, tertiary, and quaternary structures. Their biological role is regulated by their …
Spectroscopic evidences for strong hydrogen bonds with selenomethionine in proteins
Careful protein structure analysis unravels many unknown and unappreciated noncovalent
interactions that control protein structure; one such unrecognized interaction in protein is …
interactions that control protein structure; one such unrecognized interaction in protein is …
ChemPreview: an augmented reality-based molecular interface
M Zheng, MP Waller - Journal of Molecular Graphics and Modelling, 2017 - Elsevier
Human computer interfaces make computational science more comprehensible and
impactful. Complex 3D structures such as proteins or DNA are magnified by digital …
impactful. Complex 3D structures such as proteins or DNA are magnified by digital …